+++ /dev/null
-/*=========================================================================
- Program: vv http://www.creatis.insa-lyon.fr/rio/vv
-
- Authors belong to:
- - University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://www.centreleonberard.fr
- - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
-
- This software is distributed WITHOUT ANY WARRANTY; without even
- the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the copyright notices for more information.
-
- It is distributed under dual licence
-
- - BSD See included LICENSE.txt file
- - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
-#ifndef clitkDecomposeThroughErosionImageFilter_txx
-#define clitkDecomposeThroughErosionImageFilter_txx
-
-/* =================================================
- * @file clitkDecomposeThroughErosionImageFilter.txx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
-
-
-namespace clitk
-{
-
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<class InputImageType, class OutputImageType>
- DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::DecomposeThroughErosionImageFilter()
- {
- m_Verbose=false;
- m_Lower =1;
- m_Upper=1;
- m_Inside=1;
- m_Outside=0;
- m_ErosionPaddingValue=static_cast<OutputPixelType>(-1);
- for (unsigned int i=0; i<InputImageDimension; i++)
- m_Radius[i]=1;
- m_NumberOfNewLabels=1;
- m_FullyConnected=true;
- m_MinimumObjectSize=10;
- m_MinimumNumberOfIterations=1;
- }
-
-
- //-------------------------------------------------------------------
- // Update with the number of dimensions and the pixeltype
- //-------------------------------------------------------------------
- template<class InputImageType, class OutputImageType>
- void
- DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::GenerateData()
- {
-
- //---------------------------------
- // Typedefs
- //---------------------------------
-
- // Internal type
- typedef itk::Image<InternalPixelType, InputImageDimension> InternalImageType;
-
- // Filters used
- typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinaryThresholdImageFilter;
- typedef itk::BinaryBallStructuringElement<InputPixelType,InputImageDimension > KernelType;
- typedef itk::BinaryErodeImageFilter<InternalImageType, InternalImageType , KernelType> BinaryErodeImageFilterType;
- typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> BinaryThresholdImageFilterType;
- typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
- typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
- typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelImageFilterType;
- typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType> SetBackgroundImageFilterType;
-
- //---------------------------------
- // Binarize input
- //---------------------------------
- typename InputBinaryThresholdImageFilter::Pointer inputBinarizer=InputBinaryThresholdImageFilter::New();
- inputBinarizer->SetInput(this->GetInput());
- inputBinarizer->SetLowerThreshold(m_Lower);
- inputBinarizer->SetUpperThreshold(m_Upper);
- inputBinarizer ->SetInsideValue(m_Inside);
- inputBinarizer ->SetOutsideValue(m_Outside);
- if(m_Verbose) std::cout<<"Binarizing the input..."<<std::endl;
- inputBinarizer->Update();
-
- //---------------------------------
- // Label the input
- //---------------------------------
- typename ConnectFilterType::Pointer inputConnectFilter=ConnectFilterType::New();
- inputConnectFilter->SetInput(inputBinarizer->GetOutput());
- inputConnectFilter->SetBackgroundValue(0);
- inputConnectFilter->SetFullyConnected(m_FullyConnected);
- if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
- // inputConnectFilter->Update();
-
- //---------------------------------
- // Count the initial labels
- //---------------------------------
- typename StatisticsImageFilterType::Pointer inputStatisticsImageFilter=StatisticsImageFilterType::New();
- inputStatisticsImageFilter->SetInput(inputConnectFilter->GetOutput());
- if(m_Verbose) std::cout<<"Counting the initial labels..."<<std::endl;
- inputStatisticsImageFilter->Update();
- unsigned int initialNumberOfLabels= inputStatisticsImageFilter->GetMaximum();
- if(m_Verbose) std::cout<<"The input contained "<<initialNumberOfLabels<<" disctictive label(s)..."<<std::endl;
- if(m_Verbose) std::cout<<"Performing erosions till at least "<<initialNumberOfLabels+m_NumberOfNewLabels<<" distinctive labels are counted..."<<std::endl;
-
- //---------------------------------
- // Structuring element
- //---------------------------------
- KernelType structuringElement;
- structuringElement.SetRadius(m_Radius);
- structuringElement.CreateStructuringElement();
-
- //---------------------------------
- // Repeat while not decomposed
- //---------------------------------
- typename InternalImageType::Pointer current=inputBinarizer->GetOutput();
- typename InternalImageType::Pointer output=inputBinarizer->GetOutput();
- unsigned int iteration=0;
- unsigned int max =initialNumberOfLabels;
-
- while ( (iteration < m_MinimumNumberOfIterations) || ( (max< initialNumberOfLabels + m_NumberOfNewLabels ) && (iteration<100 ) ) )
- {
-
-
- if(m_Verbose) std::cout<<"Eroding image (iteration "<<iteration<<")..."<<std::endl;
-
- //---------------------------------
- // Erode
- //---------------------------------
- typename BinaryErodeImageFilterType::Pointer erosionFilter=BinaryErodeImageFilterType::New();
- erosionFilter->SetInput (current);
- erosionFilter->SetForegroundValue (1);
- erosionFilter->SetBackgroundValue (-1);
- erosionFilter->SetBoundaryToForeground(false);
- erosionFilter->SetKernel(structuringElement);
- erosionFilter->Update();
- current=erosionFilter->GetOutput();
-
- //---------------------------------
- // Binarize (remove -1)
- //---------------------------------
- typename BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
- binarizer->SetInput(erosionFilter->GetOutput());
- binarizer->SetLowerThreshold(1);
- binarizer->SetUpperThreshold(1);
- binarizer ->SetInsideValue(1);
- binarizer ->SetOutsideValue(0);
- if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
- //binarizer->Update();
-
-
- //---------------------------------
- // ReLabel the connected components
- //---------------------------------
- typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
- connectFilter->SetInput(binarizer->GetOutput());
- connectFilter->SetBackgroundValue(0);
- connectFilter->SetFullyConnected(m_FullyConnected);
- if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
- //connectFilter->Update();
-
- //---------------------------------
- // Sort
- //---------------------------------
- typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
- relabelFilter->SetInput(connectFilter->GetOutput());
- relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize);
- //relabelFilter->Update();
-
-
- //---------------------------------
- // Count the labels
- //---------------------------------
- typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
- statisticsImageFilter->SetInput(relabelFilter->GetOutput());
- statisticsImageFilter->Update();
- max= statisticsImageFilter->GetMaximum();
- if(m_Verbose) std::cout<<"Counted "<<max<<" label (s) larger then "<<m_MinimumObjectSize<<" voxels..."<<std::endl;
- output=statisticsImageFilter->GetOutput();
-
- // Next iteration
- iteration++;
- }
-
-
- //---------------------------------
- // Binarize current (remove -1)
- //---------------------------------
- typename BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
- binarizer->SetInput(current);
- binarizer->SetLowerThreshold(1);
- binarizer->SetUpperThreshold(1);
- binarizer ->SetInsideValue(1);
- binarizer ->SetOutsideValue(0);
- if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
- //binarizer->Update();
-
- //---------------------------------
- // ReLabel the connected components
- //---------------------------------
- typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
- connectFilter->SetInput(binarizer->GetOutput());
- connectFilter->SetBackgroundValue(0);
- connectFilter->SetFullyConnected(m_FullyConnected);
- if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
- connectFilter->Update();
-
- //---------------------------------
- // Sort
- //---------------------------------
- typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
- relabelFilter->SetInput(connectFilter->GetOutput());
- //relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize); // Preserve all intensities
- //relabelFilter->Update();
-
- //---------------------------------
- // Set -1 to padding value
- //---------------------------------
- typename SetBackgroundImageFilterType::Pointer setBackgroundFilter =SetBackgroundImageFilterType::New();
- setBackgroundFilter->SetInput(relabelFilter->GetOutput());
- setBackgroundFilter->SetInput2(current);
- setBackgroundFilter->SetMaskValue(-1);
- setBackgroundFilter->SetOutsideValue(m_ErosionPaddingValue);
- if(m_Verbose) std::cout<<"Setting the eroded region to "<<m_ErosionPaddingValue<<"..."<<std::endl;
-
- //---------------------------------
- // Cast
- //---------------------------------
- typedef itk::CastImageFilter<InternalImageType, OutputImageType> CastImageFilterType;
- typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
- caster->SetInput(setBackgroundFilter->GetOutput());
- caster->Update();
-
- //---------------------------------
- // SetOutput
- //---------------------------------
- this->SetNthOutput(0, caster->GetOutput());
- }
-
-
-}//end clitk
-
-#endif //#define clitkDecomposeThroughErosionImageFilter_txx
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